Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

Li, Qiujie; Su, Na; Zhang, Ling; Tong, Ru-chang; Zhang, Xiao-Hui; Wang, Junru; Chang, Zhao‐Yang; Zhao, Liang; Potter, Daniel

doi:10.1038/s41598-020-76699-7

Cited by 29 publications

(30 citation statements)

References 69 publications

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“…This result as well as those from mVISTA, SSRs, and repeat sequence analyses support that the intergenic spacers harbor the highest levels of variation in plastomes. High variability regions in the intergenic spacer have been reported in other studies and shown excellent discriminating ability, such as Echinacea of Asteraceae , Rhodiola of Crassulaceae (Zhao et al, 2019), and Pulsatilla of Ranunculaceae (Li et al, 2020). Therefore, developing specific barcodes in the intergenic spacers is well-founded and should provide a reliable approach to assess the phylogenetic relationships and identification among Maddenia species.…”

Section: On Specific Barcoding Of Maddeniamentioning

confidence: 80%

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

Liu

Wang

et al. 2021

Front. Plant Sci.

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The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

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Section: On Specific Barcoding Of Maddeniamentioning

confidence: 80%

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

Liu

Wang

et al. 2021

Front. Plant Sci.

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“…Chloroplast (cp) genomes have been widely used to infer plant phylogenetic relationships at all taxonomic levels in angiosperms because of their conserved structure, uniparental inheritance, general lack of recombination, and small effective population size (Cosner et al 2004;Wicke et al 2011). With the rapid development of next-generation sequencing, cp genomes are increasingly being used for phylogenetic relationship reconstruction (Li et al 2020a;Mu et al 2020;Zhao et al 2020;Uckele et al 2021). Since the first oak cp genome for Q. rubra was published in 2014, up to 30 species have been sequenced (Alexander & Woeste 2014;Li et al 2020b;Zhang et al 2020).…”

Section: Introductionmentioning

confidence: 99%

The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

Wang¹,

Wang²,

Kozlowski³

2021

pfs

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Quercus ningangensis is an economically and ecologically important tree species belonging to the family Fagaceae. In this study, the complete chloroplast (cp) genome of Q. ningangensis was sequenced and assembled, and 18 published cp genomes of Quercus were retrieved for genomic analyses (including sequence divergence, repeat elements, and structure) and phylogenetic inference. With this study, we found that complete cp genomes in Quercus are conserved, and we discovered a codon composition bias, which may be related to genomic content and genetic characteristics. In addition, we detected considerable structural variations in the expansion and contraction of inverted repeat regions. Six regions with relatively high variable (matK-rps16, psbC, ycf3 intron, rbcL, petA-psbJ, and ycf1) were detected by conducting a sliding window analysis, which has a high potential for developing effective genetic markers. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods resulted in a robust phylogenetic tree of Quercus with high resolution for nearly all identified nodes. The phylogenetic relationships showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta. The results of this study contribute to future research into the phylogenetic evolution of Quercus section Cyclobalanopsis (Fagaceae).

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“…Although these variations occur in both the gene region and the intergenic region, they were found more in the intergenic region than gene region [42]. In the plastomes of Polygonaceae, the number of genes, as well as the length of gene regions, are mostly similar (Table 2, Fig.…”

Section: Plastome Variationmentioning

confidence: 93%

Plastome comparison and phylogenomic of Fagopyrum (Polygonaceae): insights into detailed sequence divergence and taxonomic relationships

Liu

Wang

et al. 2022

Preprint

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Background: Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum. Results: In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768–159,985 bp) than another genus of Polygonaceae (158,851–170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence similarity showed significant differences between intra-group and inter-group.Conclusions: The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. Most of the Polygonaceae plastomes may have experienced gene loss events, resulting in the nested distribution of IR/SC boundary variation. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.

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Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

Cited by 29 publications

References 69 publications

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

Plastome comparison and phylogenomic of Fagopyrum (Polygonaceae): insights into detailed sequence divergence and taxonomic relationships

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